docs: sort the top-level directories into five sections by what the reader wants

Every docs directory moves under 1-getting-started, 2-handbook,
4-implementation or 5-project; the options reference (section 3) comes from
the website and has no directory here. trust-boundary stays whole under the
handbook for now. web-ui, swarm and tools split between handbook and
implementation, and the command-line references move to
2-handbook/reference. Links, path references in code and nix, and the docs
index follow the moves; no page content changes.

frontend/packages/agent/src/agent.css

@@ -16,7 +16,7 @@
 
 /* ─── full-screen layout overrides ─────────────────────────────────
    The agent page mounts a full-viewport terminal under a fixed
-   frosted-glass header. See docs/web-ui/agent.md::Per-agent
+   frosted-glass header. See docs/2-handbook/web-ui/agent.md::Per-agent
    page for the layer / pill / side-panel structure; rules below
    override the in-page defaults from @hive/shared. */
 
@@ -184,7 +184,7 @@ h3 {
 }
 .agent-icon {
   /* Square identity anchor — explicit 5em sizing + align-self.
-     See docs/web-ui/agent.md::Per-agent page (Agent icon) for the
+     See docs/2-handbook/web-ui/agent.md::Per-agent page (Agent icon) for the
      intrinsic-dim-pushes-parent-flex-open + sticks-to-top
      rationale. */
   width: 5em;
@@ -684,7 +684,7 @@ pre.diff {
 /* Tail pill (↓ N new): z-index bumped above the floating chrome so the
    pill sits on the top layer instead of being clipped by it. (Pill is anchored in
    `.agent-main` rather than `.terminal-wrap` — see
-   docs/web-ui/agent.md::Per-agent page Terminal-wrap paragraph for the
+   docs/2-handbook/web-ui/agent.md::Per-agent page Terminal-wrap paragraph for the
    backdrop-filter stacking-context rationale.) */
 .agent-main .tail-pill {
   bottom: 0.6em;

frontend/packages/agent/src/colors.css

@@ -2,5 +2,5 @@
    esbuild emits its own `dist/static/colors.css`, linked first by every
    agent page (before theme.css). This is the theme swap contract: a
    stylix-generated variant replaces only this file. See
-   @hive/shared/colors.css + docs/web-ui/css-vars.md. */
+   @hive/shared/colors.css + docs/4-implementation/web-ui/css-vars.md. */
 @import "@hive/shared/colors.css";

frontend/packages/agent/src/components/Header.tsx

@@ -53,7 +53,7 @@ export interface HeaderProps {
    * a variable pill count) grows to fit badges+pills together, keeping
    * the header a stable height even on widescreen. Meta-nav
    * (`<MetaNav>`) lives here too, as a fixed-size trigger, not an
-   * inline link list in the title row (docs/web-ui/agent.md). */
+   * inline link list in the title row (docs/2-handbook/web-ui/agent.md). */
   pills?: ComponentChildren;
 }
 

frontend/packages/agent/src/index.html

@@ -19,7 +19,7 @@
   <body class="agent-shell">
     <!-- The Preact rewrite owns everything below — header, terminal,
        side panel. See main.tsx/Root.tsx for the component
-       tree; docs/web-ui/agent.md for the design. -->
+       tree; docs/2-handbook/web-ui/agent.md for the design. -->
     <div id="preact-root"></div>
 
     <script type="module" src="static/main.js" defer></script>

frontend/packages/agent/src/screen.html

@@ -36,7 +36,7 @@
     <script>
       // Minimal RFB-over-WebSocket renderer. Connects to `screen/ws` on
       // the same host; the harness relays raw RFB bytes to the VNC server
-      // running inside the container. See docs/web-ui/agent.md (GET /screen)
+      // running inside the container. See docs/2-handbook/web-ui/agent.md (GET /screen)
       // for the design rationale + canvas-sizing implementation notes.
 
       (function () {
@@ -61,7 +61,7 @@
         });
 
         // --- Fit-to-window toggle ---
-        // See docs/web-ui/agent.md::Per-agent endpoints (GET /screen) for the
+        // See docs/2-handbook/web-ui/agent.md::Per-agent endpoints (GET /screen) for the
         // localStorage persistence + canvas-intrinsic-resolution +
         // pointer-rescale model.
         let fitMode = localStorage.getItem("screen-fit") !== "off";
@@ -105,7 +105,7 @@
         // Sends an RFB SetDesktopSize request so the VNC server (weston)
         // changes its actual output resolution to match the browser
         // viewport — sharper than fit-mode's CSS downscale. Gated on the
-        // server's ExtendedDesktopSize advert; see docs/web-ui/agent.md::Per-agent
+        // server's ExtendedDesktopSize advert; see docs/2-handbook/web-ui/agent.md::Per-agent
         // endpoints (GET /screen).
         let extDesktopSupported = false;
         let screenId = 1; // captured from the server's ExtendedDesktopSize advert

frontend/packages/agent/src/theme.css

@@ -2,5 +2,5 @@
    esbuild emits it as its own `dist/static/theme.css`, linked by every
    agent page right after colors.css. The base16 slots it derives from
    live in colors.css (the swap contract); a theme swap replaces only
-   that file. See @hive/shared/theme.css + docs/web-ui/css-vars.md. */
+   that file. See @hive/shared/theme.css + docs/4-implementation/web-ui/css-vars.md. */
 @import "@hive/shared/theme.css";

frontend/packages/agent/src/types.ts

@@ -40,7 +40,7 @@ export interface AgentState {
 // in the agent page header (stats/screen/forge/config + any
 // `services.hyperhive.agent.dashboardLinks` extras). `agent_links()` on the backend
 // is the single source of truth for what links an agent exposes; see
-// docs/web-ui/agent.md::Header for the kind → URL resolution table.
+// docs/2-handbook/web-ui/agent.md::Header for the kind → URL resolution table.
 export interface AgentLink {
   url: string;
   icon: string;